def main():
p = OptionParser(__doc__)
p.add_option("--levels",
help="Reorder factors, comma-delimited [default: alphabetical]")
p.add_option("--notch", default=False, action="store_true",
help="notched box plot [default: %default]")
p.add_option("--title", default=" ",
help="Title of the figure [default: %default]")
p.add_option("--xlabel", help="X-axis label [default: %default]")
p.add_option("--ylabel", help="Y-axis label [default: %default]")
p.add_option("--fontsize", default=16,
help="Font size [default: %default]")
opts, args = p.parse_args()
if len(args) != 1:
sys.exit(not p.print_help())
datafile, = args
header = open(datafile)
levels = opts.levels
xlabel = opts.xlabel
ylabel = opts.ylabel
lx, ly = header.next().rstrip().split('\t')
lx = xlabel or lx
ly = ylabel or ly
if levels:
levels = levels.split(",")
levels = ", ".join("'{0}'".format(d) for d in levels)
rtemplate = RTemplate(whisker_template, locals())
rtemplate.run()
def main():
p = OptionParser(__doc__)
p.add_option(
"--levels", help="Reorder factors, comma-delimited [default: alphabetical]"
)
p.add_option(
"--notch",
default=False,
action="store_true",
help="notched box plot",
)
p.add_option("--title", default=" ", help="Title of the figure")
p.add_option("--xlabel", help="X-axis label")
p.add_option("--ylabel", help="Y-axis label")
p.add_option("--fontsize", default=16, help="Font size")
opts, args = p.parse_args()
if len(args) != 1:
sys.exit(not p.print_help())
(datafile,) = args
header = open(datafile)
levels = opts.levels
xlabel = opts.xlabel
ylabel = opts.ylabel
lx, ly = next(header).rstrip().split("\t")
lx = xlabel or lx
ly = ylabel or ly
if levels:
levels = levels.split(",")
levels = ", ".join("'{0}'".format(d) for d in levels)
rtemplate = RTemplate(whisker_template, locals())
rtemplate.run()
def histogram_multiple(numberfiles, vmin, vmax, xlabel, title,
bins=20, skip=0, ascii=False,
facet=False, fill="white", prefix=""):
"""
Generate histogram using number from numberfile, and only numbers in the
range of (vmin, vmax). First combining multiple files.
"""
if ascii:
return texthistogram(numberfiles, vmin, vmax, title=title,
bins=bins, skip=skip)
newfile = "_".join(op.basename(x).split(".")[0] for x in numberfiles)
fw = open(newfile, "w")
print >> fw, "{0}\tgrp".format(xlabel)
for f in numberfiles:
data, va, vb = get_data(f, vmin, vmax, skip=skip)
vmin = min(vmin, va)
vmax = max(vmax, vb)
fp = open(f)
tag = op.basename(f).split(".")[0]
for row in fp:
val = row.strip()
print >> fw, "\t".join((val, tag))
fw.close()
numberfile = newfile
outfile = numberfile + '.pdf'
if prefix:
outfile = prefix + outfile
htemplate = histogram_multiple_template_b \
if facet else histogram_multiple_template_a
rtemplate = RTemplate(htemplate, locals())
rtemplate.run()
def histogram(numberfile,
vmin,
vmax,
xlabel,
title,
outfmt="pdf",
bins=50,
skip=0,
ascii=False,
base=0,
fill="white"):
"""
Generate histogram using number from numberfile, and only numbers in the
range of (vmin, vmax)
"""
if ascii:
return texthistogram([numberfile],
vmin,
vmax,
title=title,
bins=bins,
skip=skip,
base=base)
data, vmin, vmax = get_data(numberfile, vmin, vmax, skip=skip)
outfile = numberfile + ".base{0}.{1}".format(base, outfmt) \
if base else numberfile + ".pdf"
template = histogram_log_template if base else histogram_template
rtemplate = RTemplate(template, locals())
rtemplate.run()
def histogram_multiple(
numberfiles,
vmin,
vmax,
xlabel,
title,
outfmt="pdf",
tags=None,
bins=20,
skip=0,
ascii=False,
facet=False,
fill="white",
prefix="",
):
"""
Generate histogram using number from numberfile, and only numbers in the
range of (vmin, vmax). First combining multiple files.
"""
if ascii:
return texthistogram(numberfiles,
vmin,
vmax,
title=title,
bins=bins,
skip=skip)
newfile = "_".join(op.basename(x).split(".")[0] for x in numberfiles)
fw = open(newfile, "w")
print("{0}\tgrp".format(xlabel), file=fw)
if tags:
tags = tags.split(",")
for i, f in enumerate(numberfiles):
data, va, vb = get_data(f, vmin, vmax, skip=skip)
vmin = min(vmin, va)
vmax = max(vmax, vb)
fp = open(f)
if tags:
tag = tags[i]
else:
tag = op.basename(f).rsplit(".", 1)[0]
for row in fp:
val = row.strip()
print("\t".join((val, tag)), file=fw)
fw.close()
numberfile = newfile
outfile = numberfile + "." + outfmt
if prefix:
outfile = prefix + outfile
htemplate = (histogram_multiple_template_b
if facet else histogram_multiple_template_a)
rtemplate = RTemplate(htemplate, locals())
rtemplate.run()
def histogram(numberfile, vmin, vmax, xlabel, title,
bins=50, skip=0, ascii=False, log=0, fill="white"):
"""
Generate histogram using number from numberfile, and only numbers in the
range of (vmin, vmax)
"""
if ascii:
return texthistogram([numberfile], vmin, vmax, title=title,
bins=bins, skip=skip, log=log)
data, vmin, vmax = get_data(numberfile, vmin, vmax, skip=skip)
template = histogram_log_template if log else histogram_template
rtemplate = RTemplate(template, locals())
rtemplate.run()
def histogram(numberfile, vmin, vmax, xlabel, title, outfmt="pdf",
bins=50, skip=0, ascii=False, base=0, fill="white"):
"""
Generate histogram using number from numberfile, and only numbers in the
range of (vmin, vmax)
"""
if ascii:
return texthistogram([numberfile], vmin, vmax, title=title,
bins=bins, skip=skip, base=base)
data, vmin, vmax = get_data(numberfile, vmin, vmax, skip=skip)
outfile = numberfile + ".base{0}.{1}".format(base, outfmt) \
if base else numberfile + ".pdf"
template = histogram_log_template if base else histogram_template
rtemplate = RTemplate(template, locals())
rtemplate.run()
def histogram(numberfile, vmin, vmax, xlabel, title,
bins=50, skip=0, ascii=False, log=0, fill="white"):
"""
Generate histogram using number from numberfile, and only numbers in the
range of (vmin, vmax)
"""
if ascii:
return texthistogram([numberfile], vmin, vmax, title=title,
bins=bins, skip=skip, log=log)
outfile = numberfile + '.pdf'
data, vmin, vmax = get_data(numberfile, vmin, vmax, skip=skip)
base = log
template = histogram_log_template if log else histogram_template
rtemplate = RTemplate(template, locals())
rtemplate.run()
def generate_plot(filename, rplot="A50.rplot", rpdf="A50.pdf"):
from jcvi.apps.r import RTemplate
rplot_template = """
library(ggplot2)
data <- read.table("$rplot", header=T, sep="\t")
g <- ggplot(data, aes(x=index, y=cumsize, group=fasta))
g + geom_line(aes(colour=fasta)) +
xlab("Contigs") + ylab("Cumulative size (Mb)") +
opts(title="A50 plot", legend.position="top")
ggsave(file="$rpdf")
"""
rtemplate = RTemplate(rplot_template, locals())
rtemplate.run()
def generate_plot(filename, rplot="A50.rplot", rpdf="A50.pdf"):
from jcvi.apps.r import RTemplate
rplot_template = """
library(ggplot2)
data <- read.table("$rplot", header=T, sep="\t")
g <- ggplot(data, aes(x=index, y=cumsize, group=fasta))
g + geom_line(aes(colour=fasta)) +
xlab("Contigs") + ylab("Cumulative size (Mb)") +
opts(title="A50 plot", legend.position="top")
ggsave(file="$rpdf")
"""
rtemplate = RTemplate(rplot_template, locals())
rtemplate.run()